User: Vitis

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Vitis1.9k
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A plant geneticist from a taxonomist and naturalist background. Now trying to bridge classic genetics and evolutionary biology with ever-expanding genomic data and bioinformatic tools.

Posts by Vitis

<prev • 261 results • page 1 of 27 • next >
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Answer: A: data assembling and analysis for polyploid plant
... This could take an entire book to explain. I think currently the common approach is to identify and sequence the ancestral genomes, then tackle the polyploid genome, or assemble the genomes in parallel. This has generated good assemblies for canola, cotton and wheat. ...
written 1 day ago by Vitis1.9k
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Comment: C: IGB Visualization for Depth Graph
... I have not much experience with IGB, but converting BAM coverage information to BigWig (https://deeptools.readthedocs.io/en/develop/) would solve similar problems for other major genome browsers like IGV and JBrowse. ...
written 1 day ago by Vitis1.9k
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Comment: C: How to distinguish if a gene is a paralogue or an isoform?
... Not a typical bioinformatics question, but I'll give it a try. Probably both are true. This gene must have experienced duplication events (eight local or whole genome) that generated paralogous copies. Each copy may also have multiple transcription isoforms. You'll have to find the conserved regions ...
written 2 days ago by Vitis1.9k
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Answer: A: Algorithms for identification of insertion sites using split reads
... A lot of approaches to tackle this problem. A very good discussion here: https://www.biostars.org/p/225399/#363762 ...
written 6 days ago by Vitis1.9k
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Answer: A: Annovar annotation for plants
... In addition to the excellent VEP, the other option would be using SnpEff, for which you could build your custom annotation database with GTF or GFF3 and annotate the VCFs. For details see: http://snpeff.sourceforge.net/SnpEff.html ...
written 7 days ago by Vitis1.9k
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Comment: C: Identification of the sequence insertion site in the genome
... Pysam helps you fetch the CIGAR strings for reads. CIGAR strings would give you information about clipping by "S" and "H" operations. For this specific problem, insertion would generate junctions between inserts and genome. Reads spanning the junctions would have clipping because for a junction read ...
written 8 days ago by Vitis1.9k
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Comment: C: can delly identify multiple copies of a unique deletion?
... I'm a bit confused. Usually variant callers like Delly would give a "depth" parameter for the variants. Isn't that what you're looking for? Of course, "depth" is not number of copies or number of molecules, they're just related. You need other approaches to track down the number of molecules. ...
written 9 days ago by Vitis1.9k
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Assembly and consensus tools for Nanopore reads from amplicons
... I had Nanopore reads from amplicons as short as 600bp, and tried to do a quick and dirty assembly and consensus process. Both miniasm + racon and canu failed, suggesting that the reads were too short and there was no enough information for assembling. I wonder whether there is a tool that could do t ...
assembly written 13 days ago by Vitis1.9k
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Answer: A: can delly identify multiple copies of a unique deletion?
... Considering inheritance of MtDNA as haplotypes, wouldn't any heterozygosity of the deletion detected indicate some sort of mosaicism, i. e. cells containing both MtDNAs with and without the deletion? Quantifying them is a whole different problem since there probably are PCR amplifications involved ...
written 13 days ago by Vitis1.9k
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Answer: A: Get the divergence between two species with a ref genome and reads
... Divergence is not a uniform value across the genome: coding regions are restricted by stronger selection force against fast and big changes over time, while non-coding regions are less constrained. Given you could map reads from one species to reference genome from another species, your comparison s ...
written 13 days ago by Vitis1.9k

Latest awards to Vitis

Scholar 27 days ago, created an answer that has been accepted. For A: How to run SnpEff for Tomato 2.5 (S_lycopersicum_chromosomes.2.50) reference, gf
Teacher 27 days ago, created an answer with at least 3 up-votes. For A: Rna-Seq Tag Count
Scholar 6 weeks ago, created an answer that has been accepted. For A: How to run SnpEff for Tomato 2.5 (S_lycopersicum_chromosomes.2.50) reference, gf
Scholar 3 months ago, created an answer that has been accepted. For A: How to run SnpEff for Tomato 2.5 (S_lycopersicum_chromosomes.2.50) reference, gf
Scholar 4 months ago, created an answer that has been accepted. For A: How to run SnpEff for Tomato 2.5 (S_lycopersicum_chromosomes.2.50) reference, gf
Great Question 2.1 years ago, created a question with more than 5,000 views. For Mapping Rates From Bwa
Good Answer 2.1 years ago, created an answer that was upvoted at least 5 times. For A: Ka/Ks Ratio For Within A Gene - Very Confused !!
Scholar 2.1 years ago, created an answer that has been accepted. For A: How to run SnpEff for Tomato 2.5 (S_lycopersicum_chromosomes.2.50) reference, gf
Appreciated 3.6 years ago, created a post with more than 5 votes. For A: Ka/Ks Ratio For Within A Gene - Very Confused !!
Appreciated 3.6 years ago, created a post with more than 5 votes. For A: How To Convert Centimorgan To Base Pair
Good Answer 3.6 years ago, created an answer that was upvoted at least 5 times. For A: A Result From Mummer Alignment
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Housekeeping Gene Identifications
Popular Question 4.2 years ago, created a question with more than 1,000 views. For Mapping Rates From Bwa
Teacher 4.7 years ago, created an answer with at least 3 up-votes. For A: Looking For A Good Open Source Command-Line Sanger Sequence Pairwise Assembler
Autobiographer 4.9 years ago, has more than 80 characters in the information field of the user's profile.
Guru 4.9 years ago, received more than 100 upvotes.
Centurion 4.9 years ago, created 100 posts.
Supporter 4.9 years ago, voted at least 25 times.
Teacher 5.6 years ago, created an answer with at least 3 up-votes. For A: Looking For A Good Open Source Command-Line Sanger Sequence Pairwise Assembler
Appreciated 6.9 years ago, created a post with more than 5 votes. For A: Rna-Seq Data Variant Calling
Teacher 6.9 years ago, created an answer with at least 3 up-votes. For A: Rna-Seq Data Variant Calling
Student 6.9 years ago, asked a question with at least 3 up-votes. For Genomic Read Mapping Biased Towards Coding Regions?
Appreciated 7.1 years ago, created a post with more than 5 votes. For A: How To Convert Centimorgan To Base Pair
Teacher 7.1 years ago, created an answer with at least 3 up-votes. For A: How To Convert Centimorgan To Base Pair
Teacher 7.2 years ago, created an answer with at least 3 up-votes. For A: A Result From Mummer Alignment

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